Alternatives and similar repositories for TDM

Users that are interested in TDM are comparing it to the libraries listed below

• slowkow / tftargets
  Human transcription factor target genes from 6 databases in convenient R format.
  ☆86Updated 6 years ago
• montilab / hypeR
  An R Package for Geneset Enrichment Workflows
  ☆76Updated this week
• leekgroup / recount
  R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/
  ☆41Updated 8 months ago
• pachterlab / BBB
  Bioinformatics for Benched Biologists
  ☆22Updated 5 years ago
• waldronlab / data-science-seminar
  Topics In Data Science and Bioinformatics
  ☆79Updated last year
• nsheff / LOLA
  Locus Overlap Analysis: Enrichment of Genomic Ranges
  ☆78Updated 4 years ago
• rhondabacher / SCnorm
  Normalization for single cell RNA-seq data
  ☆48Updated 2 months ago
• kkdey / CountClust
  A R package for Grade of Membership model and Visualization of counts data:
  ☆32Updated 4 years ago
• francescojm / ADAM
  Adaptive Daisy Model to discriminate core-fitness/context-specific essential genes in large scale CRISPR-Cas9 screens
  ☆23Updated 6 years ago
• genesofeve / projectR
  ☆62Updated 5 months ago
• KrishnaswamyLab / phateR
  PHATE dimensionality reduction method implemented in R
  ☆78Updated 4 years ago
• SamBuckberry / RUN-WGCNA
  Wrapper R scripts for performing a weighted-gene co-expression network analysis (WGCNA)
  ☆28Updated 10 years ago
• jtleek / svaseq
  Analysis for svaseq paper
  ☆19Updated 11 years ago
• JEFworks / liger
  Lightweight Iterative Gene set Enrichment in R
  ☆57Updated 10 months ago
• ibn-salem / sevenC
  7C: Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
  ☆13Updated 6 years ago
• icbi-lab / immune_deconvolution_benchmark
  Reproducible pipeline for "Comprehensive evaluation of cell-type quantification methods for immuno-oncology", Sturm et al. 2019, https://…
  ☆43Updated 5 years ago
• leekgroup / phenopredict
  Use gene expression to predict phenotype sample information
  ☆19Updated 7 years ago
• pachterlab / scRNA-Seq-TCC-prep
  Preprocessing of single-cell RNA-Seq (deprecated)
  ☆62Updated 6 years ago
• czi-hca-comp-tools / easy-data
  easy access to benchmark datasets
  ☆50Updated 7 years ago
• wgmao / PLIER
  Pathway-Level Information Extractor (PLIER): a generative model for gene expression data
  ☆54Updated last year
• Nealelab / UKBB_ldsc
  Sample code for ldsc analyses in UKBB
  ☆31Updated 2 years ago
• sigven / oncoEnrichR
  Explore the cancer relevance of your gene list
  ☆51Updated 6 months ago
• MaayanLab / archs4
  ARCHS4 RNA-seq processing scripts and web server pages.
  ☆58Updated 4 years ago
• caravagnalab / revolver
  Tumour stratification by maximum-likelihood repeated evolution from multi-region sequencing data
  ☆65Updated 2 years ago
• leekgroup / networks_correction
  Code to reproduce analysis in "Addressing confounding artifacts in reconstruction of gene co-expression networks"
  ☆16Updated 6 years ago
• HumanCellAtlas / skylab
  Soon to be deprecated in favor of broadinstitute/warp github repo. Previously: Secondary analysis pipelines
  ☆48Updated 5 months ago
• kieranrcampbell / phenopath
  Genomic trajectories (pseudotimes) in the presence of heterogenous environmental and genetic backgrounds
  ☆10Updated 6 years ago
• ctlab / LinSeed
  Linseed: LINear Subspace identification for gene Expresion Deconvolution
  ☆31Updated last week
• cBioPortal / cgdsr
  R-Based API for accessing the MSKCC Cancer Genomics Data Server (CGDS)
  ☆25Updated 4 years ago
• Simon-Coetzee / motifBreakR
  A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites.
  ☆29Updated last year